P.W. SweeneyYale Peabody Museum of

Natural History

Mobilizing New England vascular plant data to

track environmental change

ObjectivesRationaleDigitization Plan

Organizational Structure

WorkflowMobilizationTraining &

OutreachTimeline

OUTLINE

Digitize 1.3 million N.E. vascular plant specimens from 15 regional herbaria

OBJECTIVES

The main goal of this TCN is to provide data to support the study of the consequences of climate change and land use history in the New England region over the last two centuries

RATIONALE

Why New England?HerbariaLandscapeHistoryScientists

RATIONALE: NEW ENGLAND

Climate Change

Plant phenological observations play an important role in the effort to understand the effects of rising temperatures

Our project will cater to climate-change studies by capturing phenology (flowering and leafing-out stage) data

We will develop controlled vocabularies for flowering stage and leafing-out stage

RATIONALE: THEME

Land-use historyHerbarium specimens,

representing thousands of species with diverse ecological ranges and tolerances can add critical insights into the long-term consequences of past land-use

We will capture habitat data for a subset of taxa targeted for their particular importance to land-use studies, and we will develop a controlled vocabulary for habitat

RATIONALE: THEME

Brown University (BRU)Harvard University (HUH)U. of New Hampshire

(NHA)U. of Massachusetts

Amherst (MASS)U. of Vermont (VT)Yale University (YU)

Bartlett Arboretum (BART)Berkshire Museum (BERK)Boston University (BSN)Central Connecticut State

U. (CCSU)Connecticut College

(CCNL)Harvard Forest (HF)Keene State (KESC)Western Connecticut

State U. (WCSU)Westfield State U. (WSCH)

University of Oklahoma

DIGITIZATION PLAN: ORGANIZATION

YU

BARTBER

K

BSN

KESCCCNL

CCSU

WCSU

DIGITIZATION PLAN: ORGANIZATION

MASS

WSCH

HF

BRU

HUH

NHA

VT

DIGITIZATION PLAN: ORGANIZATION

HUH & YU

BRU MASS

NHA

VT

BART

BERK

BSNKESC

CCNL

CCSU

HF

WCSU

WSCU

DIGITIZATION PLAN: ORGANIZATION

Collection Preparation

(Pre-capture)Primary

digitization

Data Enhancement (Secondary Digitization)

DIGITIZATION PLAN: WORKFLOW

In herbaria, sheets are often organized into folders by genus or species, with a single identification applying to al l specimens in that folder. Often organized by geography, as well

Capture data that reflects the physical storage structure of the collection before imaging and data basing individual specimens

Associate this pre-captured data with specimen records at a later stage

WORKFLOW: PRE-CAPTURE

WORKFLOW: PRE-CAPTURE

WORKFLOW: PRE-CAPTURE

WORKFLOW: PRE-CAPTURE

Capture an image, a barcode number, a subset of label data & associate pre-capture data with specimen occurrence records

WORKFLOW: PRIMARY DIGITIZATION

To increase the efficiency of capturing an image and specimen-level data, we will develop and test an high throughput digitization apparatus

WORKFLOW: PRIMARY DIGITIZATION

Digitization

Stations

Symbiota

TACC

WORKFLOW: PRIMARY DIGITIZATION

Specimen Data

Images

The secondary digitization stage will involve humans capturing (via keystroking) habitat and phenology data from images of specimens and labels.

WORKFLOW: SECONDARY DIGITIZATION

Georeference to at least town level

WORKFLOW: SECONDARY DIGITIZATION

Filtered

Push

Morphbank

Collection Database

s(Specify)

Symbiota

WORKFLOW: ENHANCEMENT

All of the data and images will be available to public through Consortium of Northeastern Herbaria (CNH) Symbiota portal(neherbaria.org/CNH)

MOBILIZATION

Undergraduates and graduate students engaged in digitization & collections activities

Collection internships to teens

TRAINING & OUTREACH

We will establish a network of citizen science observers to provide information on flowering and leafing-out times across the New England region

TRAINING & OUTREACH

TIMELINE

Set-up infrastructure and digitization

workflowsDevelop & test

digitization apparatuses at OU

Continued development, testing, and fine- tuning

Conduct pre- capture stage at primary institutions

Pre-capture of small collections (at MASS & YU)

Conduct Primary digitization

Conduct Secondary digitization.

Year 1 Year 2 Year 3 Year 4

Informatics Infrastructure

Pre-capture

Primary Digitizatio

n

Secondary Digitizatio

n

Publicity website, management site (Open Atrium), and portal in place (Symbiota)

Pre-capture Pre-capture application and workflow developed Process underway at participating collections

Kick-off meeting in early September Pre-capture application and workflow demonstration

Digitization apparatus in development Deployment in spring

Citizen Science project beginning recruitment process

PROGRESS

National Science Foundation

iDigBio

Symbiota Project

FilteredPush

Texas Advanced Computing Center (TACC) & The iPlant Collaborative

ACKNOWLEDGEMENTS